geneSubsets-class {Rmagpie} | R Documentation |
Forward gene selection is usually a computationally expensive task. To reduce the computation expense one may want to do not consider one gene at a time but chunks of genes. This class store the sizes of gene susbets to be tested during forward gene selection.
new("geneSubsets", optionValues)
Create a geneSubsets, the sizes of the different subsets are determined by
optionValues
. The size of the biggest subset maxSubsetSize
and
the number of subsets to be tried noOfOptions
are automatically deducted.
The speed is set to high
is there are less models than the size of the
biggest subset and 'slow' if not.
new("geneSubsets", maxSubsetSize, speed="high")
Create a geneSubsets, with a biggest subset of size maxSubsetSize
. If
the speed
is high
the sizes of the subsets are increased by a power of 2
from 1 to the biggest power of 2 smaller than maxSubsetSize
. If the
speed is slow
the sizes of the subsets are increased by 1
from 1 to the maxSubsetSize
.
maxSubsetSize
:numeric
. Size of the biggest subset
optionValues
:numeric
(vector). Sizes of the subsets in acsending order
noOfOptions
:numeric
. Total number of subsets
to be tried during backward gene selection
speed
:character
. Speed of the backward feature selection.
high
if the number of models is smaller than the size of the biggest subset,
slow
if not.
getMaxSubsetSize(geneSubsets), getMaxSubsetSize(geneSubsets)<-
Retreive and modify the size of the biggest subset (slot maxSubsetSize)
getOptionValues(geneSubsets), getOptionValues(geneSubsets)<-
Retreive and modify the sizes of the subsets of features (slot optionValues)
getNoOfOptions(geneSubsets)
Retreive the total number of subsets to be tried during backward gene selection (slot noModels)
getSpeed(geneSubsets), getSpeed(geneSubsets)<-
Retreive and modify the speed of the backward feature selection. (slot speed)
Camille Maumet
geneSubset235 <- new("geneSubsets", optionValues=c(2,3,5)) geneSubset235 getSubsetsSizes(geneSubset235) getSpeed(geneSubset235) getMaxSubsetSize(geneSubset235) geneSubsetMax60 <- new("geneSubsets", maxSubsetSize=60, speed="slow") geneSubsetMax60 geneSubsetSlow <- new("geneSubsets", maxSubsetSize=70, speed="slow") geneSubsetSlow getMaxSubsetSize(geneSubsetMax60) <- 70 geneSubsetMax60 newSizes <- c(1,2,3,4,5) getSubsetsSizes(geneSubsetMax60) <- newSizes geneSubsetMax60 getSpeed(geneSubset235) <- 'slow' geneSubset235